- A lot of code cleaned up; separated metrics code from AlleleFrequencyMetricsWalker into AlleleMetrics and eliminated the former class. AFMW (aside from being a name so long that it warrants an acronym) can now be implemented by passing an option to AlleleFreqeuncyWalker that logs metrics to a file.
- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface - Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk
parent
c6ab60ee04
commit
e3ac0cb500
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
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import org.broadinstitute.sting.playground.utils.AlleleMetrics;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.*;
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import org.apache.log4j.Logger;
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@ -15,11 +16,13 @@ import java.util.Arrays;
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import java.util.Random;
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import java.io.PrintStream;
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public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>
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public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>// implements AllelicVariant
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{
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@Argument public int N;
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@Argument(required=false,defaultValue="0") public int DOWNSAMPLE;
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@Argument public String GFF_OUTPUT_FILE;
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@Argument(shortName="met", doc="Turns on logging of metrics on the fly with AlleleFrequency calculation") public boolean LOG_METRICS;
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@Argument(required=false, defaultValue="", doc="Name of file where metrics will output") public String METRICS_OUTPUT_FILE;
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protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
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@ -30,7 +33,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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{
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// Convert context data into bases and 4-base quals
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String bases = getBases(context);
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double quals[][] = getOneBaseQuals(context);
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double quals[][] = getQuals(context);
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/*
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// DEBUG: print the data for a read
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@ -87,7 +90,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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}
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assert(altnum != -1);
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AlleleFrequencyEstimate alleleFreq = AlleleFrequencyEstimator(context.getLocation().toString(), N, bases.getBytes(), quals, refnum, altnum, bases.length());
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AlleleFrequencyEstimate alleleFreq = AlleleFrequencyEstimator(context.getLocation(), N, bases.getBytes(), quals, refnum, altnum, bases.length());
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alleleFreq.notes = String.format("A:%d C:%d G:%d T:%d",
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base_counts[nuc2num['A']],
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@ -108,6 +111,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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logger.debug(String.format(" => result is %s", alleleFreq));
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if (LOG_METRICS) metrics.nextPosition(alleleFreq, rodData);
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return alleleFreq;
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}
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@ -128,7 +133,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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return new String(bases);
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}
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static public double[][] getOneBaseQuals (LocusContext context)
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static public double[][] getQuals (LocusContext context)
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{
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int numReads = context.getReads().size(); //numReads();
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double[][] quals = new double[numReads][4];
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@ -155,13 +160,13 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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}else{
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assert (SQ_field instanceof byte[]);
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byte[] hex_quals = (byte[]) SQ_field;
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System.out.printf("SQ field (hex): %s\n", bytesToHexString(hex_quals));
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System.out.printf("SAM record: %s\n", read.format());
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//System.out.printf("SQ field (hex): %s\n", bytesToHexString(hex_quals));
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//System.out.printf("SAM record: %s\n", read.format());
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int hex_qual = hex_quals[offset];
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int called2num = hex_qual & 0x3;
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double qual2 = (double)(hex_qual >> 2) / 100.0;
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System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
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//System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
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quals[i][called2num] = qual2;
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//
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@ -191,7 +196,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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return (char) ((value < 10) ? ('0' + value) : ('A' + value - 10));
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}
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public AlleleFrequencyEstimate AlleleFrequencyEstimator(String location, int N, byte[] bases, double[][] quals, int refnum, int altnum, int depth)
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public AlleleFrequencyEstimate AlleleFrequencyEstimator(GenomeLoc location, int N, byte[] bases, double[][] quals, int refnum, int altnum, int depth)
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{
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// q = hypothetical %nonref
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@ -251,7 +256,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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Arrays.sort(bestMixtures);
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// Calculate Lod of the mixture versus other possible
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// Answers how confident are we in the best mixture versus the next best mixture
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// Answers how confident are we in the best mixture versus the nextPosition best mixture
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double lodBestVsNextBest = bestMixtures[0].posterior - bestMixtures[1].posterior;
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AlleleFrequencyEstimate alleleFreq = new AlleleFrequencyEstimate(location,
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@ -375,48 +380,42 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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return result;
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}
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private String confident_ref_interval_start = "";
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private String confident_ref_interval_contig = "";
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private long confident_ref_interval_start = 0;
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private double confident_ref_interval_LOD_sum = 0;
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private double confident_ref_interval_length = 0;
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private int last_position_considered = -1;
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private long last_position_considered = -1;
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private boolean inside_confident_ref_interval = false;
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AlleleMetrics metrics;
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public String reduceInit()
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{
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confident_ref_interval_start = "";
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confident_ref_interval_contig = "";
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confident_ref_interval_start = 0;
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confident_ref_interval_LOD_sum = 0;
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confident_ref_interval_length = 0;
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last_position_considered = -1;
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inside_confident_ref_interval = false;
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return "";
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if (LOG_METRICS) metrics = new AlleleMetrics("SNTH");//METRICS_OUTPUT_FILE);
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return "";
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}
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public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
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{
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// Print RESULT data for confident calls
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String[] tokens;
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tokens = alleleFreq.location.split(":");
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int current_offset = Integer.parseInt(tokens[1]);
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long current_offset = alleleFreq.location.getStart(); //Integer.parseInt(tokens[1]);
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if (inside_confident_ref_interval &&
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((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)) )
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{
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// No longer hom-ref, so output a ref line.
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tokens = confident_ref_interval_start.split(":");
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String contig = tokens[0];
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int start = Integer.parseInt(tokens[1]);
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tokens = alleleFreq.location.split(":");
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int end = last_position_considered;
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double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
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output.format("%s\tCALLER\tREFERENCE\t%d\t%d\t%f\t.\t.\tLENGTH %d\n",
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contig,
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start,
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end,
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confident_ref_interval_contig,
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confident_ref_interval_start,
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last_position_considered,
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lod,
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(int)(confident_ref_interval_length));
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@ -435,7 +434,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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else if ((!inside_confident_ref_interval) && (alleleFreq.lodVsRef <= -5.0))
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{
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// We moved into a hom-ref region so start a new interval.
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confident_ref_interval_start = alleleFreq.location;
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confident_ref_interval_contig = alleleFreq.location.getContig();
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confident_ref_interval_start = alleleFreq.location.getStart();
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confident_ref_interval_LOD_sum = alleleFreq.lodVsRef;
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confident_ref_interval_length = 1;
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inside_confident_ref_interval = true;
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@ -444,6 +444,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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last_position_considered = current_offset;
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if (alleleFreq.lodVsRef >= 5) { this.output.print(alleleFreq.asGFFString()); }
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if (LOG_METRICS) metrics.printMetricsAtLocusIntervals(1000);
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return "";
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}
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@ -492,17 +493,13 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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if (inside_confident_ref_interval)
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{
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// if we have a confident reference interval still hanging open, close it.
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String tokens[] = confident_ref_interval_start.split(":");
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String contig = tokens[0];
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int start = Integer.parseInt(tokens[1]);
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int end = last_position_considered;
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double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
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output.format("%s\tCALLER\tREFERENCE\t%d\t%d\t%f\t.\t.\tLENGTH %d\n",
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contig,
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start,
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end,
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confident_ref_interval_contig,
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confident_ref_interval_start,
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last_position_considered,
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lod,
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(int)(confident_ref_interval_length));
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@ -522,6 +519,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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e.printStackTrace();
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System.exit(-1);
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}
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if (LOG_METRICS) metrics.printMetrics();
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}
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static void print_base_qual_matrix(double [][]quals) {
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@ -569,7 +568,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
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{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0}};
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AlleleFrequencyWalker w = new AlleleFrequencyWalker();
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AlleleFrequencyEstimate estimate = w.AlleleFrequencyEstimator("null", N, het_bases, het_quals, 0, 1, 20);
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AlleleFrequencyEstimate estimate = w.AlleleFrequencyEstimator(null, N, het_bases, het_quals, 0, 1, 20);
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System.out.print(String.format("50%% Het : %s %c %c %f %f %f %d %s\n",
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"null", estimate.ref, estimate.alt, estimate.qhat, estimate.qstar, estimate.lodVsRef, 20, "null"));
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}
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@ -686,7 +685,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
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int N = 10;
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AlleleFrequencyWalker w = new AlleleFrequencyWalker();
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w.N = 10;
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AlleleFrequencyEstimate estimate = w.AlleleFrequencyEstimator("null", N, het_bases, het_quals, 0, 1, 20);
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AlleleFrequencyEstimate estimate = w.AlleleFrequencyEstimator(null, N, het_bases, het_quals, 0, 1, 20);
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System.out.print(String.format("10%% Het : %s %c %c %f %f %f %d %s\n",
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"null", estimate.ref, estimate.alt, estimate.qhat, estimate.qstar, estimate.lodVsRef, 20, "null"));
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}
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@ -0,0 +1,27 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: andrewk
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* Date: Apr 2, 2009
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* Time: 9:01:44 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class AlleleMetricsWalker {
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// Class that will walk over various metrics in a reference ordered way
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// This class walks over the genome in reference order and calls AlleleMetrics on each class
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// Hapmap and dbSNP tracks are taken from the command line
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// At first pass, this will at least be able to walk over a GFF file and compare to the hapmap and dbsnp
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// tracks specified on the command line and handed in via the LocusContext
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public void map(List<AllelicVariant> avdata) {
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}
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}
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@ -1,10 +1,11 @@
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package org.broadinstitute.sting.playground.utils;
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import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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public class AlleleFrequencyEstimate {
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//AlleleFrequencyEstimate();
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public String location;
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public GenomeLoc location;
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public char ref;
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public char alt;
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public int N;
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@ -15,7 +16,9 @@ public class AlleleFrequencyEstimate {
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public int depth;
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public String notes;
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public AlleleFrequencyEstimate(String location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, int depth)
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GenomeLoc l;
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public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, int depth)
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{
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this.location = location;
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this.ref = ref;
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@ -31,12 +34,10 @@ public class AlleleFrequencyEstimate {
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public String asGFFString()
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{
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String[] tokens;
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tokens = location.split(":");
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return String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\tREF %c\t;\tALT %c\t;\tFREQ %f\n",
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tokens[0],
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tokens[1],
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tokens[1],
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location.getContig(),
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location.getStart(),
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location.getStart(),
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lodVsRef,
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ref,
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alt,
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@ -1,25 +1,21 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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package org.broadinstitute.sting.playground.utils;
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import org.broadinstitute.sting.gatk.refdata.rodGFF;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.gatk.refdata.rodGFF;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
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import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
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import java.util.List;
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import java.io.PrintStream;
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/**
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* Created by IntelliJ IDEA.
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* User: andrewk
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* Date: Mar 18, 2009
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* Time: 5:28:58 PM
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* Date: Apr 1, 2009
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* Time: 5:53:21 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEstimate, String>
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{
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public class AlleleMetrics {
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long dbsnp_hits=0;
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long num_variants=0;
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@ -31,12 +27,24 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
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long hapmap_refvar_correct = 0;
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long hapmap_refvar_incorrect = 0;
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AlleleFrequencyWalker caller;
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protected PrintStream out;
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public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context)
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{
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AlleleFrequencyEstimate alleleFreq = caller.map(rodData, ref, context);
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public AlleleMetrics(String MetricsOutputFile) {
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try
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{
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/*if ( MetricsOutputFile.equals("-") )
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this.out = out;
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else*/
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this.out = new PrintStream(MetricsOutputFile);
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}
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catch (Exception e)
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{
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e.printStackTrace();
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System.exit(-1);
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}
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}
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public void nextPosition(AlleleFrequencyEstimate alleleFreq, List<ReferenceOrderedDatum> rodData) {
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num_loci_total += 1;
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boolean is_dbSNP_SNP = false;
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@ -47,7 +55,7 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
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{
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if ( datum != null )
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{
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if ( datum instanceof rodDbSNP )
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if ( datum instanceof rodDbSNP)
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{
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rodDbSNP dbsnp = (rodDbSNP)datum;
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if (dbsnp.isSNP()) is_dbSNP_SNP = true;
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@ -64,9 +72,9 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
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if (Math.abs(alleleFreq.lodVsRef) >= LOD_cutoff) { num_loci_confident += 1; }
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if (alleleFreq.qstar > 0.0 && alleleFreq.lodVsRef >= LOD_cutoff)
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{
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{
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// Confident variant.
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num_variants += 1;
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if (is_dbSNP_SNP)
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@ -105,7 +113,8 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
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hapmap_genotype_correct++;
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}else{
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hapmap_genotype_incorrect++;
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System.out.printf(" INCORRECT GENOTYPE Bases: %s", AlleleFrequencyWalker.getBases(context));
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//System.out.printf(" INCORRECT GENOTYPE Bases: %s", AlleleFrequencyWalker.getBases(context));
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System.out.printf(" INCORRECT GENOTYPE");
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//AlleleFrequencyWalker.print_base_qual_matrix(AlleleFrequencyWalker.getOneBaseQuals(context));
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}
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}
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@ -118,16 +127,14 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
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boolean called_var = alleleFreq.qstar != 0.0;
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if (hapmap_q != -1 && hapmap_var != called_var) {
|
||||
hapmap_refvar_incorrect++;
|
||||
System.out.printf(" INCORRECT REFVAR CALL");
|
||||
}else{
|
||||
hapmap_refvar_correct++;
|
||||
System.out.printf(" INCORRECT REFVAR CALL Bases: %s\n", AlleleFrequencyWalker.getBases(context));
|
||||
}
|
||||
}
|
||||
|
||||
out.print("\n");
|
||||
}
|
||||
|
||||
return alleleFreq;
|
||||
}
|
||||
|
||||
public void printMetrics()
|
||||
|
|
@ -159,23 +166,9 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
|
|||
out.println();
|
||||
}
|
||||
|
||||
public void onTraversalDone(String result)
|
||||
{
|
||||
printMetrics();
|
||||
public void printMetricsAtLocusIntervals(int loci_interval) {
|
||||
if (num_loci_total % loci_interval == 0) printMetrics();
|
||||
}
|
||||
|
||||
public String reduceInit()
|
||||
{
|
||||
caller = new AlleleFrequencyWalker();
|
||||
return "";
|
||||
}
|
||||
|
||||
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
|
||||
{
|
||||
if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asGFFString()); }
|
||||
if (this.num_loci_total % 1000 == 0) { printMetrics(); }
|
||||
return "null";
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue